Variant report

Variant	rs2009972
Chromosome Location	chr15:52106301-52106302
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52105030..52107341-chr15:52262781..52264487,2	MCF-7	breast:
2	chr15:52100222..52103696-chr15:52103888..52107125,3	MCF-7	breast:
3	chr15:52105390..52107839-chr15:52134954..52136621,2	K562	blood:
4	chr15:52097000..52098593-chr15:52105503..52107331,2	K562	blood:
5	chr15:52100848..52103641-chr15:52104210..52107534,4	K562	blood:
6	chr15:52106284..52108941-chr15:52129387..52131261,2	MCF-7	breast:
7	chr15:52103958..52107915-chr15:52115684..52119713,4	MCF-7	breast:
8	chr15:52104389..52106808-chr15:52121747..52123928,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000138594	Chromatin interaction
ENSG00000166477	Chromatin interaction

Extended variants
information (count: 185 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:183)

rs_ID	r²[population]
rs1001690	0.81[CEU][hapmap]
rs1025184	0.89[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap]
rs1035737	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs1035739	0.82[ASN][1000 genomes]
rs10444823	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs10775145	0.86[CHB][hapmap];0.91[CHD][hapmap];0.82[TSI][hapmap]
rs10851504	0.82[EUR][1000 genomes]
rs11049	0.91[CEU][hapmap]
rs11070865	0.89[CEU][hapmap];0.84[TSI][hapmap]
rs11070868	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs1133883	0.89[CEU][hapmap]
rs11630084	0.86[CHB][hapmap]
rs11630579	0.91[CEU][hapmap]
rs11630943	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs11636345	0.86[CHB][hapmap];0.91[CHD][hapmap];0.82[TSI][hapmap]
rs11637876	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs11638820	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs12438686	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs12593708	0.92[CEU][hapmap]
rs12903707	0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs12905283	0.89[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs12908327	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs12915015	0.87[CEU][hapmap]
rs12915568	0.89[CEU][hapmap]
rs12917133	0.86[CHB][hapmap];0.93[CHD][hapmap];0.82[TSI][hapmap]
rs1545602	0.86[CHB][hapmap]
rs17526463	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs17526760	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs17611193	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs17705732	0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs1811326	0.91[CHB][hapmap];0.86[CHD][hapmap];0.82[TSI][hapmap]
rs1840708	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs1863430	0.89[CEU][hapmap]
rs1867984	0.91[CHB][hapmap]
rs1972689	0.91[CHB][hapmap];0.86[CHD][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs1991267	0.89[CEU][hapmap]
rs2007335	0.89[CEU][hapmap]
rs2007355	0.85[CEU][hapmap];0.89[TSI][hapmap]
rs2010026	0.89[CEU][hapmap]
rs2011995	0.89[CEU][hapmap]
rs2014638	0.82[TSI][hapmap]
rs2034856	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs2034857	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs2034858	0.86[CHB][hapmap];0.91[CHD][hapmap];0.82[TSI][hapmap]
rs2052705	0.88[CEU][hapmap]
rs2052706	0.91[CEU][hapmap]
rs2052708	0.89[CEU][hapmap]
rs2052709	0.89[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2114191	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs2241503	0.85[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs2252606	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2252831	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs2253116	0.89[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.84[ASN][1000 genomes]
rs2258248	0.89[CEU][hapmap]
rs2264339	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs2414119	0.83[ASN][1000 genomes]
rs2433217	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs2433221	0.85[CEU][hapmap];0.89[TSI][hapmap]
rs2436655	0.89[CEU][hapmap]
rs2436656	0.95[CEU][hapmap]
rs2436658	0.82[ASN][1000 genomes]
rs2436660	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs2436661	0.83[ASN][1000 genomes]
rs2441780	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs2448946	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs2448950	0.89[CEU][hapmap]
rs2448953	0.88[CEU][hapmap]
rs2470602	0.82[ASN][1000 genomes]
rs2470603	0.82[ASN][1000 genomes]
rs2470604	0.82[ASN][1000 genomes]
rs2470605	0.80[ASN][1000 genomes]
rs2470607	0.80[ASN][1000 genomes]
rs2470612	0.88[CEU][hapmap];0.87[TSI][hapmap]
rs2470617	0.85[CEU][hapmap]
rs2554305	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs2554306	0.83[ASN][1000 genomes]
rs2554307	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs2554308	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs2554314	0.88[CEU][hapmap]
rs2554315	0.81[CHB][hapmap];0.93[CHD][hapmap]
rs2554327	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs2554336	0.91[CHB][hapmap];0.86[CHD][hapmap];0.80[MEX][hapmap]
rs2554342	0.84[ASN][1000 genomes]
rs2554348	0.96[CEU][hapmap];0.81[CHB][hapmap];0.88[EUR][1000 genomes]
rs2554349	0.89[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.84[ASN][1000 genomes]
rs2554350	0.84[ASN][1000 genomes]
rs2570224	0.82[TSI][hapmap]
rs2570228	0.91[CHB][hapmap];0.86[CHD][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs2570231	0.83[ASN][1000 genomes]
rs2570233	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs2570238	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2570239	0.89[CEU][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs2570240	0.82[EUR][1000 genomes]
rs2570241	0.89[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs2570258	0.91[CHB][hapmap];0.86[CHD][hapmap];0.80[MEX][hapmap]
rs2570263	0.82[ASN][1000 genomes]
rs2570268	0.84[ASN][1000 genomes]
rs2570269	0.82[ASN][1000 genomes]
rs2570271	0.82[ASN][1000 genomes]
rs2570275	0.84[ASN][1000 genomes]
rs2593170	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs2593173	0.89[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.84[ASN][1000 genomes]
rs2593179	0.82[ASN][1000 genomes]
rs2593181	0.89[CEU][hapmap]
rs2593183	0.84[ASN][1000 genomes]
rs2593185	0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2593187	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2593188	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs2593198	0.84[ASN][1000 genomes]
rs2593199	0.88[CEU][hapmap]
rs2593202	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2593204	0.82[ASN][1000 genomes]
rs2623254	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs2623255	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs2623271	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs2623279	0.84[ASN][1000 genomes]
rs2623281	0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2623282	0.89[CEU][hapmap]
rs2623283	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2623286	0.83[ASN][1000 genomes]
rs2623288	0.84[ASN][1000 genomes]
rs2623289	0.82[ASN][1000 genomes]
rs2912186	0.89[CEU][hapmap]
rs2912187	0.92[CEU][hapmap]
rs2912189	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs2916169	0.88[CEU][hapmap]
rs2916172	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs2916176	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs2916177	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs2929423	0.89[CEU][hapmap]
rs2929424	0.89[CEU][hapmap]
rs2929425	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs2929426	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs2959285	0.92[CEU][hapmap];0.89[TSI][hapmap]
rs2959293	0.85[CEU][hapmap];0.89[TSI][hapmap]
rs2959296	0.92[CEU][hapmap]
rs2959298	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs2959299	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs3751596	0.86[CHB][hapmap];0.93[CHD][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs3794532	0.89[CEU][hapmap]
rs3794534	0.86[CHB][hapmap]
rs3794535	0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[TSI][hapmap];0.82[ASN][1000 genomes]
rs3794536	0.83[ASN][1000 genomes]
rs4238383	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs4774602	0.86[CHB][hapmap];0.91[CHD][hapmap];0.82[TSI][hapmap]
rs4775978	0.84[CHB][hapmap]
rs4775982	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs4775983	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[TSI][hapmap];0.82[ASN][1000 genomes]
rs58758283	0.82[ASN][1000 genomes]
rs60329909	0.83[ASN][1000 genomes]
rs6493519	0.86[CHB][hapmap]
rs6493520	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs6493521	0.89[CEU][hapmap]
rs6493522	0.83[ASN][1000 genomes]
rs6493523	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6493525	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs6493526	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs689884	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs690638	0.81[CHB][hapmap];0.91[CHD][hapmap]
rs7162554	0.81[ASN][1000 genomes]
rs7162925	0.88[CEU][hapmap]
rs7163541	0.89[CEU][hapmap]
rs7165283	0.86[CHB][hapmap]
rs7168659	0.89[CEU][hapmap]
rs7170091	0.88[CEU][hapmap]
rs7171459	0.82[ASN][1000 genomes]
rs7171796	0.89[CEU][hapmap]
rs7174497	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs7174808	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs7178561	0.89[CEU][hapmap]
rs7178776	0.89[CEU][hapmap]
rs7179599	0.88[CEU][hapmap]
rs7181540	0.89[CEU][hapmap]
rs7181553	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs726158	0.89[CEU][hapmap]
rs8028890	0.86[CHB][hapmap]
rs8028922	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs8035173	0.81[CEU][hapmap]
rs8038344	0.89[CEU][hapmap]
rs8041268	0.82[ASN][1000 genomes]
rs9635308	0.81[CHB][hapmap]
rs990665	0.84[ASN][1000 genomes]
rs9944235	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv3361968	chr15:52087428-52107237	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2009972	SCG3	cis	Temporal Cortex	GTEx
rs2009972	TMOD2	cis	cerebellum	SCAN
rs2009972	SCG3	cis	Cerebellum	GTEx
rs2009972	SCG3	cis	Frontal Cortex	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52052600-52106600	Weak transcription	HSMM	muscle
2	chr15:52061600-52112000	Weak transcription	NHLF	lung
3	chr15:52085800-52108800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:52089000-52106400	Weak transcription	HSMMtube	muscle
5	chr15:52089200-52107200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr15:52091200-52109400	Weak transcription	Gastric	stomach
7	chr15:52091800-52108200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:52092000-52107800	Weak transcription	Fetal Muscle Leg	muscle
9	chr15:52093800-52108600	Weak transcription	Fetal Lung	lung
10	chr15:52098400-52106800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:52098800-52108800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr15:52099200-52107400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr15:52099200-52108800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:52099400-52107200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr15:52099600-52108600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr15:52099600-52108800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr15:52099800-52108400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr15:52099800-52109000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr15:52099800-52109400	Weak transcription	Spleen	Spleen
20	chr15:52099800-52110000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:52099800-52110400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:52099800-52110400	Weak transcription	Left Ventricle	heart
23	chr15:52099800-52113800	Weak transcription	Aorta	Aorta
24	chr15:52100000-52109400	Weak transcription	Esophagus	oesophagus
25	chr15:52100000-52109400	Weak transcription	Fetal Stomach	stomach
26	chr15:52100000-52109400	Weak transcription	Lung	lung
27	chr15:52100000-52110200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:52100000-52113200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr15:52100200-52109400	Weak transcription	Fetal Brain Female	brain
30	chr15:52100400-52108400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr15:52100600-52109800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr15:52101000-52107200	Weak transcription	Fetal Thymus	thymus
33	chr15:52101200-52108800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr15:52101200-52110200	Weak transcription	NHDF-Ad	bronchial
35	chr15:52101400-52106400	Weak transcription	Brain Germinal Matrix	brain
36	chr15:52101600-52113000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr15:52101800-52110200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:52102000-52108400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr15:52102000-52108400	Weak transcription	Brain Substantia Nigra	brain
40	chr15:52102000-52113400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:52102400-52108200	Weak transcription	Fetal Intestine Large	intestine
42	chr15:52102400-52109000	Weak transcription	Adipose Nuclei	Adipose
43	chr15:52103000-52108000	Weak transcription	Fetal Intestine Small	intestine
44	chr15:52103000-52109000	Weak transcription	Colon Smooth Muscle	Colon
45	chr15:52103000-52111600	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr15:52103600-52107000	Strong transcription	Primary T cells from cord blood	blood
47	chr15:52104000-52107000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr15:52104000-52107000	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr15:52104000-52107600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr15:52104400-52106800	Weak transcription	Brain Anterior Caudate	brain

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